2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 import static jalview.util.UrlConstants.DB_ACCESSION;
25 import static jalview.util.UrlConstants.DELIM;
26 import static jalview.util.UrlConstants.SEP;
27 import static jalview.util.UrlConstants.SEQUENCE_ID;
29 import jalview.util.MessageManager;
30 import jalview.util.UrlConstants;
31 import jalview.util.UrlLink;
33 import java.util.ArrayList;
34 import java.util.HashMap;
35 import java.util.Iterator;
36 import java.util.List;
38 import java.util.Map.Entry;
39 import java.util.StringTokenizer;
43 * Implements the UrlProviderI interface for a UrlProvider object which serves
44 * custom URLs defined by the user
49 public class CustomUrlProvider extends UrlProviderImpl
51 // Default sequence URL link label for SRS
52 private static final String SRS_LABEL = "SRS";
54 // map of string ids to urlLinks (selected)
55 private HashMap<String, UrlLink> selectedUrls;
57 // map of string ids to urlLinks (not selected)
58 private HashMap<String, UrlLink> nonselectedUrls;
61 * Construct UrlProvider for custom (user-entered) URLs
63 * @param inMenuUrlList
64 * list of URLs set to be displayed in menu, in form stored in Cache.
65 * i.e. SEP delimited string
66 * @param storedUrlList
67 * list of custom URLs entered by user but not currently displayed in
68 * menu, in form stored in Cache
70 public CustomUrlProvider(String inMenuUrlList, String storedUrlList)
74 selectedUrls = parseUrlStrings(inMenuUrlList);
75 nonselectedUrls = parseUrlStrings(storedUrlList);
76 } catch (Exception ex)
79 .println(ex.getMessage() + "\nError parsing sequence links");
84 * Construct UrlProvider for custom (user-entered) URLs
87 * list of URLs to be displayed in menu, as (label,url) pairs
88 * @param storedUrlList
89 * list of custom URLs entered by user but not currently displayed in
90 * menu, as (label,url) pairs
92 public CustomUrlProvider(Map<String, String> inMenuUrlList,
93 Map<String, String> storedUrlList)
97 selectedUrls = parseUrlList(inMenuUrlList);
98 nonselectedUrls = parseUrlList(storedUrlList);
99 } catch (Exception ex)
102 .println(ex.getMessage() + "\nError parsing sequence links");
106 private HashMap<String, UrlLink> parseUrlStrings(String urlStrings)
108 // cachedUrlList is in form <label>|<url>|<label>|<url>...
109 // parse cachedUrlList into labels (used as id) and url links
110 HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
112 StringTokenizer st = new StringTokenizer(urlStrings, SEP);
113 while (st.hasMoreElements())
115 String name = st.nextToken();
117 if (!isMiriamId(name))
119 // this one of our custom urls
120 String url = st.nextToken();
121 // check for '|' within a regex
122 int rxstart = url.indexOf(DELIM + DB_ACCESSION + DELIM);
125 rxstart = url.indexOf(DELIM + SEQUENCE_ID + DELIM);
127 while (rxstart == -1 && url.indexOf("/=" + DELIM) == -1
128 && st.hasMoreTokens())
130 url = url + SEP + st.nextToken();
132 urls.put(name, new UrlLink(name, url, name));
135 upgradeOldLinks(urls);
139 private HashMap<String, UrlLink> parseUrlList(Map<String, String> urlList)
141 HashMap<String, UrlLink> urls = new HashMap<String, UrlLink>();
147 Iterator<Map.Entry<String, String>> it = urlList.entrySet().iterator();
150 Map.Entry<String, String> pair = it.next();
151 urls.put(pair.getKey(),
152 new UrlLink(pair.getKey(), pair.getValue(), pair.getKey()));
154 upgradeOldLinks(urls);
159 * Upgrade any legacy links which may have been left lying around
161 private void upgradeOldLinks(HashMap<String, UrlLink> urls)
163 boolean upgrade = false;
164 // upgrade old SRS link
165 if (urls.containsKey(SRS_LABEL))
167 urls.remove(SRS_LABEL);
170 // upgrade old EBI link - easier just to remove and re-add than faffing
171 // around checking exact url
172 if (urls.containsKey(UrlConstants.DEFAULT_LABEL))
174 // note because this is called separately for selected and nonselected
175 // urls, the default url will not always be present
176 urls.remove(UrlConstants.DEFAULT_LABEL);
181 UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING);
182 link.setLabel(UrlConstants.DEFAULT_LABEL);
183 urls.put(UrlConstants.DEFAULT_LABEL, link);
188 public List<String> getLinksForMenu()
190 List<String> links = new ArrayList<String>();
191 Iterator<Map.Entry<String, UrlLink>> it = selectedUrls.entrySet()
195 Map.Entry<String, UrlLink> pair = it.next();
196 links.add(pair.getValue().toString());
202 public List<UrlLinkDisplay> getLinksForTable()
204 ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
205 displayLinks = getLinksForTable(selectedUrls, true);
206 displayLinks.addAll(getLinksForTable(nonselectedUrls, false));
210 private ArrayList<UrlLinkDisplay> getLinksForTable(
211 HashMap<String, UrlLink> urlList, boolean selected)
213 return super.getLinksForTable(urlList, null, selected);
217 public boolean setPrimaryUrl(String id)
219 if (selectedUrls.containsKey(id))
223 else if (nonselectedUrls.containsKey(id))
232 return (primaryUrl != null);
236 public String writeUrlsAsString(boolean selected)
238 StringBuffer links = new StringBuffer();
239 HashMap<String, UrlLink> urls;
246 urls = nonselectedUrls;
250 for (Entry<String, UrlLink> entry : urls.entrySet())
252 links.append(entry.getValue().toString());
257 links.setLength(links.length() - 1);
263 return links.toString();
267 public String getPrimaryUrl(String seqid)
269 String result = super.getPrimaryUrl(seqid, selectedUrls);
272 result = super.getPrimaryUrl(seqid, nonselectedUrls);
278 public String getPrimaryUrlId()
284 public String getPrimaryTarget(String seqid)
286 return selectedUrls.get(primaryUrl).getTarget();
290 public void setUrlData(List<UrlLinkDisplay> links)
292 HashMap<String, UrlLink> unselurls = new HashMap<String, UrlLink>();
293 HashMap<String, UrlLink> selurls = new HashMap<String, UrlLink>();
295 Iterator<UrlLinkDisplay> it = links.iterator();
298 UrlLinkDisplay link = it.next();
300 // MIRIAM ids will be handled by a different UrlProvider class
301 if (!isMiriamId(link.getId()))
303 // don't allow duplicate key names as entries will be overwritten
304 if (unselurls.containsKey(link.getId())
305 || selurls.containsKey(link.getId()))
307 throw new IllegalArgumentException(MessageManager.formatMessage(
308 "exception.url_cannot_have_duplicate_id", link.getId()));
310 if (link.getIsSelected())
312 selurls.put(link.getId(), new UrlLink(link.getDescription(),
313 link.getUrl(), link.getDescription()));
317 unselurls.put(link.getId(), new UrlLink(link.getDescription(),
318 link.getUrl(), link.getDescription()));
320 // sort out primary and selected ids
321 if (link.getIsPrimary())
323 setPrimaryUrl(link.getId());
328 nonselectedUrls = unselurls;
329 selectedUrls = selurls;
333 public String choosePrimaryUrl()
335 // unilaterally set the primary id to the EMBL_EBI link
336 if ((!nonselectedUrls.containsKey(UrlConstants.DEFAULT_LABEL))
337 && (!selectedUrls.containsKey(UrlConstants.DEFAULT_LABEL)))
339 UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING);
340 link.setLabel(UrlConstants.DEFAULT_LABEL);
341 selectedUrls.put(UrlConstants.DEFAULT_LABEL, link);
343 primaryUrl = UrlConstants.DEFAULT_LABEL;
344 return UrlConstants.DEFAULT_LABEL;
348 public boolean contains(String id)
350 return (selectedUrls.containsKey(id)
351 || nonselectedUrls.containsKey(id));